On-demand importing of a package
Just for the records, the solution was to make the matrix 'dgCmatrix" instead of 'dsCmatrix', 'dgCmatrix' works and 'dsCmatrix' does not. I suspect that this has to do something with the S4 class hierarchy in Matrix, but I am not sure. This is a quite ugly workaround, since it depends on some internal Matrix features, so I might end up just importing Matrix, as many of you suggested in the first place.... However, I agree with Gabor Grotherdieck that the issue is still there, in general. Another example would be (optionally) using the 'snow' (or now 'parallel') package. I would like to add optional parallel processing to some of my functions in a package, without actually requiring the installation of snow/parallel. If snow is there and the user wants to use it, then it is used, otherwise not. Actually, 'snow' works similarly. It (optionally) calls function from the Rmpi package, but Rmpi is only suggested, there is no hard dependency. This seems to work well for snow, but in my case I the S4 features in Matrix interfere. Gabor
On Tue, Nov 22, 2011 at 8:09 PM, G?bor Cs?rdi <csardi at rmki.kfki.hu> wrote:
Dear Martin, thanks a lot, this all makes sense and looks great. I suspected some S4 trickery and totally forgot that the base package is imported automatically. Unfortunately I still get Error in callGeneric() : ?'callGeneric' must be called from a generic function or method for my real function, but it works fine for the toy f() function, so I think I can sort this out from here. Best Regards, Gabor On Tue, Nov 22, 2011 at 6:57 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
On 11/22/2011 03:06 PM, G?bor Cs?rdi wrote:
On Tue, Nov 22, 2011 at 4:27 PM, Martin Morgan<mtmorgan at fhcrc.org> ?wrote: [...]
No need to Depend:. Use Imports: Matrix plus in the NAMESPACE file ?importFrom(Matrix, rowSums) Why do you not want to do this? Matrix is available for everyone, Imports: doesn't influence the package search path. There is a cost associated with loading the library in the first place, but...?
Not just loading, installing a package has a cost, too. Dependencies are bad, they might make my package fail, and I have no control over them. It's not just 'Matrix', I have this issue with other packages as well. Anyway, 'Imports: Matrix' is just a workaround I think. Or is the example in my initial mail expected to fail? Why is that? Why can I call some functions from 'Matrix' that way and why can't I call others?
I'm more into black-and-white -- it either needs Matrix or not; apparently it does.
It's a matter of opinion, I guess. I find it very annoying when I need to install a bunch of packages from which I don't use any code, just because some tiny bit of a package I need uses them. I would like to spare my users from this. [...]
In another message you mention
Matrix:::rowSums(W)
Error in callGeneric() :
?'callGeneric' must be called from a generic function or method
but something else is going on -- you don't get to call methods directly;
you're getting Matrix::rowSums (it's exported, so no need for a :::, see
getNamespaceExports("Matrix")). Maybe traceback() after the error would
be
insightful?
Another poster suggested this, that's why I tried. It is clear that I
should not call it directly. All I want to do is having a function
like this:
f<- function() {
?if (require(Matrix)) {
? ?res<- sparseMatrix(dims=c(5, 5), i=1:5, j=1:5, x=1:5)
?} else {
? ?res<- diag(1:5)
?}
?y<- rowSums(res)
?res / y
}
Setting the subjective bit, about depending or not, aside, is there
really no solution for this? The code in the manual page examples work
fine without importing the package and just loading it if needed and
available. Why doesn't the code within the package?
If I create a package that does not Import: Matrix (btw, Matrix is distributed with all R), with only a function f, and with exports(f) in NAMESPACE, I get
library(pkgA) f()
Loading required package: Matrix Loading required package: lattice Attaching package: 'Matrix' The following object(s) are masked from 'package:base': ? ?det Error in rowSums(res) : 'x' must be an array of at least two dimensions This is because (a) Matrix is attached to the user search path but (b) because f is defined in the NAMESPACE of pkgA, rowSums is looked for first in the pkgA NAMESPACE, and in then in the search of the package (which includes base) and then in the user search path. It is found in base, and the search ends there. If I modify f to use ?y <- Matrix::rowSums(res) I get
f()
Loading required package: Matrix Loading required package: lattice Attaching package: 'Matrix' The following object(s) are masked from 'package:base': ? ?det 5 x 5 sparse Matrix of class "dgCMatrix" [1,] 1 . . . . [2,] . 1 . . . [3,] . . 1 . . [4,] . . . 1 . [5,] . . . . 1 I start off with the correct rowSums, and continue from there. Martin
Thanks for the patience, Gabor
Martin
[...]
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-- Gabor Csardi <csardi at rmki.kfki.hu>? ?? MTA KFKI RMKI
Gabor Csardi <csardi at rmki.kfki.hu>? ?? MTA KFKI RMKI